Phenotype QC

1 Probands

• Note that the measurement of sum and mean is similar, thus only sum is presented.
• 13 Primary Variables
• 12 Secondary Variables
• Adjusted by Age, Sex, Chip, FSIQ (with or without) and then rank-based invserse normalise transformed (RINT).

1.1 Primary Variables

1.1.1 Not Adjusted

grid.raster(readPNG("figures/primary_probands_Notadj.png"))

Sample Sizes (Levels of phenotypes) are shown.

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1.1.2 Adjusted

1.1.2.1 PCs Excluded

grid.raster(readPNG("figures/primary_probands_adj.png"))

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1.1.2.2 PCs Included

grid.raster(readPNG("figures/primary_probands_adjAndPCs.png"))

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1.2 Secondary Variables

1.2.1 Not Adjusted

grid.raster(readPNG("figures/secondary_probands_Notadj.png"))

Sample Sizes (Levels of phenotypes) are shown.

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1.2.2 Adjusted

1.2.2.1 PCs Excluded

grid.raster(readPNG("figures/secondary_probands_adj.png"))

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1.2.2.2 PCs Included

grid.raster(readPNG("figures/secondary_probands_adjAndPCs.png"))

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2 Unaffected Siblings

• 7 shared phenotypes betwen Probands and Unaffected Siblings
• 3 Primary Variables
• 4 Secondary Variables
• Adjusted by Sex, Chip and then RINT.

2.1 Not Adjusted

grid.raster(readPNG("figures/UnaffSibs_shared_Notadj.png"))

Sample Sizes (Levels of phenotypes) are shown.

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2.2 Adjusted

2.2.1 PCs Excluded

grid.raster(readPNG("figures/UnaffSibs_shared_adj.png"))

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2.2.2 PCs Included

grid.raster(readPNG("figures/UnaffSibs_shared_adjAndPCs.png"))

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3 Probands & Unaffected Siblings

• 7 shared phenotypes of Probands and Unaffected Siblings
• show phenotype distribution both separately and combined

3.1 Separated

3.1.1 Raw

grid.raster(readPNG("figures/probandsAndunaffSibs_raw.png"))

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3.1.2 PCs Excluded

3.1.2.1 Fitting IQ

grid.raster(readPNG("figures/probandsAndunaffSibs_adjIQ.png"))

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3.1.2.2 Not Fitting IQ

grid.raster(readPNG("figures/probandsAndunaffSibs_adjnoIQ.png"))

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3.1.3 PCs Included

3.1.3.1 Fitting IQ

grid.raster(readPNG("figures/probandsAndunaffSibs_adjIQ_withPCs.png"))

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3.1.3.2 Not Fitting IQ

grid.raster(readPNG("figures/probandsAndunaffSibs_adjnoIQ_withPCs.png"))

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3.2 Combined

3.2.1 Raw

grid.raster(readPNG("figures/probandsAndunaffSibs_rawII.png"))

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3.2.2 PCs Excluded

3.2.2.1 Fitting IQ

grid.raster(readPNG("figures/probandsAndunaffSibs_adjIQII.png"))

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3.2.2.2 Not Fitting IQ

grid.raster(readPNG("figures/probandsAndunaffSibs_adjnoIQII.png"))

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3.2.3 PCs Included

3.2.3.1 Fitting IQ

grid.raster(readPNG("figures/probandsAndunaffSibs_adjIQII_withPCs.png"))

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3.2.3.2 Not Fitting IQ

grid.raster(readPNG("figures/probandsAndunaffSibs_adjnoIQII_withPCs.png"))

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